This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch debian-experimental
in repository seqan2.
commit 2dc4b734116abba149190b545eefe074165da933
Author: Michael R. Crusoe <michael.cru...@gmail.com>
Date: Fri Jan 13 05:33:08 2017 -0800
new upstream release
---
debian/changelog | 5 +-
debian/patches/series | 3 -
debian/patches/spelling.patch | 1155 -----------------------------------------
debian/patches/tandem-rename | 54 --
debian/patches/typo-fix | 22 -
5 files changed, 3 insertions(+), 1236 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index f572649..1f4e786 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,10 @@
-seqan2 (2.3.0~1.20161019~af07bc1+dfsg-5) UNRELEASED; urgency=medium
+seqan2 (2.3.1+dfsg-1) experimental; urgency=medium
* Try to save more memory on kfreebsd-*
* Fix parallel build disabling to not produce warnings
+ * New upstream release, three incorporated patched removed
- -- Michael R. Crusoe <michael.cru...@gmail.com> Wed, 26 Oct 2016 05:51:51
-0700
+ -- Michael R. Crusoe <michael.cru...@gmail.com> Fri, 13 Jan 2017 05:36:28
-0800
seqan2 (2.3.0~1.20161019~af07bc1+dfsg-4) experimental; urgency=medium
diff --git a/debian/patches/series b/debian/patches/series
index 94e4c15..fe8c345 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,2 @@
-tandem-rename
-typo-fix
-spelling.patch
short-description
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644
index c500480..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,1155 +0,0 @@
-From: Michael R. Crusoe <michael.cru...@gmail.com>
-Subject: Fix some spelling issues
-Forwarded: https://github.com/seqan/seqan/pull/1872
---- seqan2.orig/apps/rabema/rabema_evaluate.cpp
-+++ seqan2/apps/rabema/rabema_evaluate.cpp
-@@ -91,7 +91,7 @@
- // original position of this read.
- bool oracleMode;
-
-- // Consider only reads that have a unique match in the mapping result
file. Usefull for precision computation.
-+ // Consider only reads that have a unique match in the mapping result
file. Useful for precision computation.
- bool onlyUniqueReads;
-
- // The benchmark category, one of {"all", "any-best", "all-best"}.
-@@ -142,7 +142,7 @@
- // Print the missed intervals to stderr for debugging purposes.
- bool showMissedIntervals;
-
-- // Print superflous intervals (intervals found in BAM file but have too
bad score).
-+ // Print superfluous intervals (intervals found in BAM file but have too
bad score).
- bool showSuperflousIntervals;
-
- // Print additional intervals (intervals found in BAM with good score
that are not in WIT file).
-@@ -1093,7 +1093,7 @@
- "sample position. For simulated
data."));
- addOption(parser, seqan::ArgParseOption("", "only-unique-reads",
- "Consider only reads that a
single alignment in the mapping result file. "
-- "Usefull for precision
computation."));
-+ "Useful for precision
computation."));
- addOption(parser, seqan::ArgParseOption("", "match-N", "When set, N
matches all characters without penalty."));
- addOption(parser, seqan::ArgParseOption("", "distance-metric",
- "Set distance metric. Valid
values: hamming, edit. Default: edit.",
-@@ -1278,7 +1278,7 @@
- << " additional " <<
yesNo(options.showAdditionalIntervals) << '\n'
- << " hit " << yesNo(options.showHitIntervals)
<< '\n'
- << " missed " <<
yesNo(options.showMissedIntervals) << '\n'
-- << " superflous " <<
yesNo(options.showSuperflousIntervals) << '\n'
-+ << " superfluous " <<
yesNo(options.showSuperflousIntervals) << '\n'
- << " try hit " <<
yesNo(options.showTryHitIntervals) << '\n'
- << "\n";
-
-@@ -1430,7 +1430,7 @@
- if (!empty(options.outTsvPath))
- {
- std::cerr << '\n'
-- << "Writting output TSV " << options.outTsvPath << "
...";
-+ << "Writing output TSV " << options.outTsvPath << "
...";
- std::ofstream tsvOut(toCString(options.outTsvPath), std::ios::out |
std::ios::binary);
- bool failed = false;
- if (!tsvOut.good())
---- seqan2.orig/apps/razers3/razers.cpp
-+++ seqan2/apps/razers3/razers.cpp
-@@ -437,7 +437,7 @@
- addOption(parser, ArgParseOption("mf", "mismatch-file", "Write mismatch
patterns to \\fIFILE\\fP.", ArgParseOption::STRING, "FILE"));
-
- addSection(parser, "Misc Options");
-- addOption(parser, ArgParseOption("cm", "compact-mult", "Multiply
compaction treshold by this value after reaching and compacting.",
ArgParseOption::DOUBLE));
-+ addOption(parser, ArgParseOption("cm", "compact-mult", "Multiply
compaction threshold by this value after reaching and compacting.",
ArgParseOption::DOUBLE));
- setMinValue(parser, "compact-mult", "0");
- setDefaultValue(parser, "compact-mult", options.compactMult);
- addOption(parser, ArgParseOption("ncf", "no-compact-frac", "Don't compact
if in this last fraction of genome.", ArgParseOption::DOUBLE));
---- seqan2.orig/apps/samcat/README
-+++ seqan2/apps/samcat/README
-@@ -6,7 +6,7 @@
-
- DESCRIPTION
- This tool reads a set of input files in SAM or BAM format and outputs the
concatenation of them. If the output
-- file name is ommitted the result is written to standard output in SAM
format.
-+ file name is omitted the result is written to standard output in SAM
format.
-
- (c) Copyright 2014 by David Weese.
-
---- seqan2.orig/apps/samcat/samcat.cpp
-+++ seqan2/apps/samcat/samcat.cpp
-@@ -174,7 +174,7 @@
- addDescription(parser, "This tool reads a set of input files in SAM
format "
- #endif
- "and outputs the concatenation of them. "
-- "If the output file name is ommitted the result is
written to stdout.");
-+ "If the output file name is omitted the result is
written to stdout.");
-
- addDescription(parser, "(c) Copyright in 2014 by David Weese.");
-
---- seqan2.orig/apps/fiona/compute_gain.cpp
-+++ seqan2/apps/fiona/compute_gain.cpp
-@@ -111,7 +111,7 @@
- // Number of errors pre-correction/post-correction.
- uint64_t numErrorsPre;
- uint64_t numErrorsPost;
-- // Number of errorneous reads pre-correction/post-correction.
-+ // Number of erroneous reads pre-correction/post-correction.
- uint64_t numErrorReadsPre;
- uint64_t numErrorReadsPost;
- uint64_t numReads;
-@@ -1124,7 +1124,7 @@
- std::cerr << "WARNING: Files not read completely!\n";
- if (error)
- {
-- std::cerr << "An error occured. Bailing out.\n";
-+ std::cerr << "An error occurred. Bailing out.\n";
- return 1;
- }
-
---- seqan2.orig/apps/fiona/fiona.cpp
-+++ seqan2/apps/fiona/fiona.cpp
-@@ -2609,20 +2609,20 @@
- double median = 0.0;
- double mediumTotalOccs = 0.0;
-
-- std::map<unsigned, unsigned> vectorOccurences;
-+ std::map<unsigned, unsigned> vectorOccurrences;
-
- goBegin(iter);
- for (; !atEnd(iter); ++iter)
- {
- unsigned numOccs = countOccurrences(iter);
-- ++vectorOccurences[numOccs];
-+ ++vectorOccurrences[numOccs];
- totalOccs += numOccs;
- }
-
- mediumTotalOccs = totalOccs / 2.0;
-
- std::map<unsigned,unsigned>::iterator iterMap;
-- for (iterMap = vectorOccurences.begin (); iterMap !=
vectorOccurences.end (); ++iterMap)
-+ for (iterMap = vectorOccurrences.begin (); iterMap !=
vectorOccurrences.end (); ++iterMap)
- {
- sumMedian += iterMap->second*iterMap->first;
- if (sumMedian >= mediumTotalOccs)
-@@ -4199,7 +4199,7 @@
- String<double> sd;
- standardDeviation(sd, store.readSeqStore, options.genomeLength);
-
-- /*The strictness value allows to estimate the confidence intervall*/
-+ /*The strictness value allows one to estimate the confidence
intervall*/
- for (unsigned i = 0; i < length(options.expectedTheoretical); ++i)
- {
- double expectedTemporary = options.expectedTheoretical[i] -
options.strictness * sd[i];
-@@ -5268,7 +5268,7 @@
- // Parallelization Options.
- addSection(parser, "Parallelization Options");
-
-- addOption(parser, seqan::ArgParseOption("nt", "num-threads", "Number of
threds to use (default 1).",
-+ addOption(parser, seqan::ArgParseOption("nt", "num-threads", "Number of
threads to use (default 1).",
- seqan::ArgParseArgument::INTEGER,
"INT"));
- setMinValue(parser, "num-threads", "1");
- setDefaultValue(parser, "num-threads", options.numThreads);
---- seqan2.orig/apps/mason2/README.mason_splicing
-+++ seqan2/apps/mason2/README.mason_splicing
-@@ -19,7 +19,7 @@
- 1. Overview
- ------------------------------------------------------------------------------
-
--Mason Splicing allows to construct transcripts from a GFF/GTF file, a
-+Mason Splicing allows one to construct transcripts from a GFF/GTF file, a
- reference sequence and an optional variant file.
-
- ------------------------------------------------------------------------------
---- seqan2.orig/apps/ngs_roi/project_spliced.h
-+++ seqan2/apps/ngs_roi/project_spliced.h
-@@ -31,7 +31,7 @@
- // ==========================================================================
- // Author: Manuel Holtgrewe <manuel.holtgr...@fu-berlin.de>
- // ==========================================================================
--// The ProjectSplicedRoi class allows to do the projection of ROIs to grouped
-+// The ProjectSplicedRoi class allows one to do the projection of ROIs to
grouped
- // GTF/GFF intervals.
- //
- // This mode is enabled when the --gff-group-by KEY option is used. In this
---- seqan2.orig/apps/pair_align/pair_align.cpp
-+++ seqan2/apps/pair_align/pair_align.cpp
-@@ -33,7 +33,7 @@
- addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fB-s\\fP \\fIIN\\fP");
- setCategory(parser, "Sequence Alignment");
- addDescription(parser,
-- "The program allows to align two sequences using dyamic
programming alignment algorithms while "
-+ "The program allows one to align two sequences using
dyamic programming alignment algorithms while "
- "tweaking various parameters.");
-
- addSection(parser, "Main Options");
---- seqan2.orig/apps/rabema/README
-+++ seqan2/apps/rabema/README
-@@ -112,7 +112,7 @@
- alignments. The number of additional hits is 0. This is the number of hits in
- the read mapper output with a valid error rate (below 3% in this case) that
- are not found in the gold standard. If this number is greater than zero then
--an error occured while building the gold standard or in the evaluation
-+an error occurred while building the gold standard or in the evaluation
- program. If you get such a number then please contact the Rabema authors.
-
- The total number of reads is 8,840, the number of reads having an alignment
-@@ -136,4 +136,4 @@
- Contact
- ------
-
-- Manuel Holtgrewe <manuel.holtgr...@fu-berlin.de>
-\ No newline at end of file
-+ Manuel Holtgrewe <manuel.holtgr...@fu-berlin.de>
---- seqan2.orig/apps/rabema/rabema_build_gold_standard.cpp
-+++ seqan2/apps/rabema/rabema_build_gold_standard.cpp
-@@ -986,7 +986,7 @@
- "[\\fIOPTIONS\\fP] \\fB--out-gsi\\fP \\fIOUT.gsi\\fP
\\fB--reference\\fP \\fIREF.fa\\fP "
- "\\fB--in-bam\\fP \\fIPERFECT.{sam,bam}\\fP");
- addDescription(parser,
-- "This program allows to build a RABEMA gold standard. The
input is a reference FASTA file "
-+ "This program allows one to build a RABEMA gold standard.
The input is a reference FASTA file "
- "and a perfect SAM/BAM map (e.g. created using RazerS 3 in
full-sensitivity mode).");
- addDescription(parser,
- "The input SAM/BAM file must be \\fIsorted by
coordinate\\fP. The program will create a "
---- seqan2.orig/apps/rabema/ref_id_mapping.h
-+++ seqan2/apps/rabema/ref_id_mapping.h
-@@ -24,7 +24,7 @@
- // file. The order in the BAM file might not be the same as in the FASTA
- // file.
- //
--// The function rebuildMapping() allows to rebuild the mapping from two
-+// The function rebuildMapping() allows one to rebuild the mapping from two
- // name store caches.
- // ==========================================================================
-
---- seqan2.orig/apps/sak/README
-+++ seqan2/apps/sak/README
-@@ -1,6 +1,6 @@
- Swiss Army Knife tool... It slices and dices and makes the laundry!
-
--This tool allows to cut sequences and parts of sequences out of sequence
-+This tool allows one to cut sequences and parts of sequences out of sequence
- files. It supports all formats supported by the AutoSeqFormat class from
- SeqAn, including FASTA, FASTQ and QSeq (Illumina format).
-
---- seqan2.orig/apps/seqcons2/seqcons.cpp
-+++ seqan2/apps/seqcons2/seqcons.cpp
-@@ -92,7 +92,7 @@
- }
- catch (std::runtime_error & e)
- {
-- std::cerr << "\nERROR: An error occured during the program's
execution:\n"
-+ std::cerr << "\nERROR: An error occurred during the program's
execution:\n"
- << " " << e.what() << "\n";
- return 1;
- }
---- seqan2.orig/dox/pages/index.dox
-+++ seqan2/dox/pages/index.dox
-@@ -40,7 +40,7 @@
- <tr><td><ul><li>@link localAlignment
@endlink</li></ul></td><td></td></tr>
- <tr><td><ul><li>@link LocalAlignmentEnumerator
@endlink</li></ul></td><td>offers the Waterman-Eggert algorithm for enumerating
suboptimal local alignments</td></tr>
- <tr><td><ul><li>@link Align @endlink</li></ul></td><td>provides a
data structure for tabular alignment of sequences with the same type</td></tr>
-- <tr><td><ul><li>@link Gaps @endlink</li></ul></td><td>allows to
store gaps independent of the underlying sequence</td></tr>
-+ <tr><td><ul><li>@link Gaps @endlink</li></ul></td><td>allows one
to store gaps independent of the underlying sequence</td></tr>
- </table>
- </li>
- <li>
---- seqan2.orig/dox/pages/language_entities.dox
-+++ seqan2/dox/pages/language_entities.dox
-@@ -16,7 +16,7 @@
-
- @htmlonly <h2 data-lang-entity="typedef" id="typedef">Typedef</h2>
@endhtmlonly
-
--<strong>Typedefs are a common, standardized C++ language feature that allows
to give custom names to arbitrary types.</strong>
-+<strong>Typedefs are a common, standardized C++ language feature that allows
one to give custom names to arbitrary types.</strong>
-
- When programming SeqAn, they are often used for giving short names to
complicated, nested template instantiations or to the result of a <a
href="#metafunction">metafunction</a>.
-
---- seqan2.orig/include/seqan/align/gaps_base.h
-+++ seqan2/include/seqan/align/gaps_base.h
-@@ -112,7 +112,7 @@
- * @tparam TSequence The type of the underlying sequence.
- * @tparam TSpec Tag for specialization.
- *
-- * Gaps wrap a @link ContainerConcept Sequence @endlink and allows to (1)
insert gaps into the sequence and (2) select
-+ * Gaps wrap a @link ContainerConcept Sequence @endlink and allows one to (1)
insert gaps into the sequence and (2) select
- * an infix of the gapped sequence (clipping). The gaps are not inserted
into the underlying sequence (source) but
- * stored separately. Using the clipping is optional and meant for selecting
parts of the alignment as a part of the
- * result of a local alignment algorithm.
---- seqan2.orig/include/seqan/arg_parse/tool_doc.h
-+++ seqan2/include/seqan/arg_parse/tool_doc.h
-@@ -568,7 +568,7 @@
- *
- * @section Remarks
- *
-- * This class is generally not used directly by the user but through @link
ArgumentParser @endlink. It allows to store
-+ * This class is generally not used directly by the user but through @link
ArgumentParser @endlink. It allows one to store
- * and represent all information related to a command line tool that would
normally go into a man page. It can be
- * printed to STL streams in different formats, currently plain text, HTML
and man pages are supported.
- *
---- seqan2.orig/include/seqan/basic/iterator_zip.h
-+++ seqan2/include/seqan/basic/iterator_zip.h
-@@ -82,7 +82,7 @@
- * @tparam TIteratorTypes A template parameter pack with one or more @link
ContainerConcept#Iterator @endlink types.
- *
- * This iterator ties together different iterator types for different
containers of the same size.
-- * It allows to operate on a single iterator, if multiple containers need to
be traversed simultaneously.
-+ * It allows one to operate on a single iterator, if multiple containers need
to be traversed simultaneously.
- * Note, that all operations are still executed in a serial fashion.
- * If the zip iterator is dereferenced it returns a <a
href="http://en.cppreference.com/w/cpp/utility/tuple";>std::tuple</a>
- * containing the dereferenced values of all embedded iterators.
---- seqan2.orig/include/seqan/basic/metaprogramming_enable_if.h
-+++ seqan2/include/seqan/basic/metaprogramming_enable_if.h
-@@ -252,7 +252,7 @@
- * @param TCondition Boolean type, one of <tt>True</tt> and <tt>False</tt> or
a metafunction returning such a tag
- * type. If <tt>True</tt> then the constructor is visible,
otherwise, it is not.
- *
-- * This macro allows to bind the visibility of a construtor to a boolean
expression by using the <a
-+ * This macro allows one to bind the visibility of a construtor to a boolean
expression by using the <a
- *
href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error";>SFINAE</a>
principle for an optional argument with default value. The macro call must be
used as the last dummy-argument of a constructor.
- *
- * To avoid an unused argument warning, call
<tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
-@@ -280,7 +280,7 @@
- * @param TCondition Boolean type, one of <tt>True</tt> and <tt>False</tt> or
a metafunction returning such a tag
- * type. If <tt>False</tt> then the constructor is
visible, otherwise, it is not.
- *
-- * This macro allows to bind the visibility of a construtor to a boolean
expression by using the <a
-+ * This macro allows one to bind the visibility of a construtor to a boolean
expression by using the <a
- *
href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error";>SFINAE</a>
principle for an optional argument with default value. The macro call must be
used as the last dummy-argument of a constructor.
- *
- * To avoid an unused argument warning, call
<tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
-@@ -309,7 +309,7 @@
- * type. If <tt>True</tt> then the function is visible,
otherwise, it is not.
- * @param TResult The type that the function should have as the return
type in case it is enabled.
- *
-- * This macro allows to bind the visibility of a construtor to a boolean
expression by using the <a
-+ * This macro allows one to bind the visibility of a construtor to a boolean
expression by using the <a
- *
href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error";>SFINAE</a>
principle for an optional argument with default value. The macro call must
occur as the return type definition of the function.
- *
- * To avoid an unused argument warning, call
<tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
-@@ -338,7 +338,7 @@
- * type. If <tt>False</tt> then the function is visible,
otherwise, it is not.
- * @param TResult The type that the function should have as the return
type in case it is enabled.
- *
-- * This macro allows to bind the visibility of a construtor to a boolean
expression by using the <a
-+ * This macro allows one to bind the visibility of a construtor to a boolean
expression by using the <a
- *
href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error";>SFINAE</a>
principle for an optional argument with default value. The macro call must
occur as the return type definition of the function.
- *
- * To avoid an unused argument warning, call
<tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
---- seqan2.orig/include/seqan/index/index_esa_base.h
-+++ seqan2/include/seqan/index/index_esa_base.h
-@@ -169,7 +169,7 @@
- typedef MaxRepeats_<void> MaxRepeats; // maximal repeat
- struct MaxRepeatOccurrences;
- typedef MaxRepeats_<MultiMems_> MultiMems; // Multiple Maximal
Exact Match
-- struct MultiMemOccurences; // i.e. maximal
match over different sequences
-+ struct MultiMemOccurrences; // i.e. maximal
match over different sequences
-
-
- /*!
-@@ -197,7 +197,7 @@
- template <typename TSize>
- struct VertexEsa {
- Pair<TSize> range; // current SA interval of hits (unique
node identifier)
-- TSize parentRight; // right boundary of parent node's range
(allows to go right)
-+ TSize parentRight; // right boundary of parent node's range
(allows one to go right)
-
-
- VertexEsa() : range(0, 0), parentRight(0) {}
---- seqan2.orig/include/seqan/index/index_esa_stree.h
-+++ seqan2/include/seqan/index/index_esa_stree.h
-@@ -335,7 +335,7 @@
- typedef typename HistoryStack_<Iter>::Type TStack;
- typedef Iter iterator;
-
-- TStack history; // contains all previously visited
intervals (allows to go up)
-+ TStack history; // contains all previously visited
intervals (allows one to go up)
-
- //____________________________________________________________________________
-
---- seqan2.orig/include/seqan/index/index_wotd.h
-+++ seqan2/include/seqan/index/index_wotd.h
-@@ -323,7 +323,7 @@
- TSize parentRepLen; // representative length of parent node
- TSize edgeLen; // length of edge above current node
- Pair<TSize> range; // current SA interval of hits
-- TSize parentRight; // right boundary of parent node's range
(allows to go right)
-+ TSize parentRight; // right boundary of parent node's range
(allows one to go right)
-
- VertexWotdModified_() :
- node(0),
---- seqan2.orig/include/seqan/parallel/parallel_splitting.h
-+++ seqan2/include/seqan/parallel/parallel_splitting.h
-@@ -58,7 +58,7 @@
- * to parallelize large for-loops that iterate over a contiguous range of
elements. The interval and the number of
- * subintervals can be set in the constructor @link Splitter::Splitter
@endlink. @link Splitter#length @endlink and
- * @link Splitter#resize @endlink can be used to retrieve or change the
number of subintervals later. In contrast to
-- * other containers the Splitter allows to access one more element than its
length would imply to allow to retrieve the
-+ * other containers the Splitter allows one to access one more element than
its length would imply to allow to retrieve the
- * right boundary of each subinterval (see example code below).
- *
- * @section Examples
---- seqan2.orig/include/seqan/sequence/sequence_interface.h
-+++ seqan2/include/seqan/sequence/sequence_interface.h
-@@ -1101,7 +1101,7 @@
- * @return TSize The amount of the requested capacity that was available.
That is the function returns the minimum of
- * <tt>newCapacity</tt> and <tt>capacity(me)</tt>.
- *
-- * This function allows to increase the capacity but not the length of a
container.
-+ * This function allows one to increase the capacity but not the length of a
container.
- *
- * Use @link StringConcept#resize @endlink if you want to change the size of
a container.
- *
---- seqan2.orig/include/seqan/sequence/string_set_base.h
-+++ seqan2/include/seqan/sequence/string_set_base.h
-@@ -69,7 +69,7 @@
- * chromosomes of a genome. This facilitates writing generic data structures
and algorithms to operate on single
- * strings and genomes which is captured by the @link TextConcept @endlink.
- *
-- * Second, the @link DependentStringSet @endlink specialization allows to
create subsets of string sets without
-+ * Second, the @link DependentStringSet @endlink specialization allows one to
create subsets of string sets without
- * storing copies of strings and identifying strings by a common id.
- *
- * @section Examples
---- seqan2.orig/include/seqan/tabix_io/tabix_index_tbi.h
-+++ seqan2/include/seqan/tabix_io/tabix_index_tbi.h
-@@ -33,7 +33,7 @@
- // ==========================================================================
- // (Read-only) Tabix index support.
- //
--// A Tabix index (Heng Li) allows to randomly seek in a tab-seperated genome
-+// A Tabix index (Heng Li) allows one to randomly seek in a tab-seperated
genome
- // related file, e.g. VCF, GFF, SAM, BED, etc. The corresponding file only
- // needs to be sorted by chromosomal position in advance and optionally
- // compressed with 'bgzip'. The resulting file must be indexed with 'tabix'.
---- seqan2.orig/manual/attic/Tutorial/IndicesOld.rst
-+++ seqan2/manual/attic/Tutorial/IndicesOld.rst
-@@ -3,7 +3,7 @@
- Indices
- -------
-
--A substring index is a datatype which allows to seek efficiently for all
-+A substring index is a datatype which allows one to seek efficiently for all
- occurrences of a pattern in a string or a set of strings. Substring
- indices are very efficient for the exact string matching problem, i.e.
- finding all exact occurrences of a pattern in a text or a text
---- seqan2.orig/tests/basic/test_basic_allocator.h
-+++ seqan2/tests/basic/test_basic_allocator.h
-@@ -49,7 +49,7 @@
- // ==========================================================================
-
- // The following helper class is passed as the parent allocator to all tested
--// allocators. It allows to count the number of allocations and deallocations
-+// allocators. It allows one to count the number of allocations and
deallocations
- // and checks whether all allocated memory blocks are correctly deallocated
- // when it is destructed.
-
---- seqan2.orig/tests/realign/test_realign.cpp
-+++ seqan2/tests/realign/test_realign.cpp
-@@ -42,7 +42,7 @@
- static const bool PRINT_REALIGNMENTS = false;
- static const bool DEBUG_REALIGNMENT = false;
-
--// Helper function that allows to add gaps into the i-th read alignment in a
fragmentStore.
-+// Helper function that allows one to add gaps into the i-th read alignment
in a fragmentStore.
- template <typename TFragmentStore>
- void addGaps(TFragmentStore & store, unsigned alignID, unsigned pos)
- {
---- seqan2.orig/apps/fiona/error_rate_from_sam.cpp
-+++ seqan2/apps/fiona/error_rate_from_sam.cpp
-@@ -71,7 +71,7 @@
- unsigned totalReadCount = 0; // Number of reads read.
- unsigned totalErrorneousReadCount = 0; // Number of reads with errors
read, excluding unaligned reads.
- unsigned totalUnalignedReadCount = 0; // Number of reads without
alignments.
-- std::map<unsigned, unsigned> histo; // Histogram error count -> num
occurences.
-+ std::map<unsigned, unsigned> histo; // Histogram error count -> num
occurrences.
-
- // Read records
-
-@@ -153,7 +153,7 @@
- std::cout << "STATISTICS\n"
- << "total read count " << totalReadCount << "\t\t(excludes
unaligned reads)\n"
- << "unaligned read count " << totalUnalignedReadCount << "\n"
-- << "errorneous read count " << totalErrorneousReadCount << "\n"
-+ << "erroneous read count " << totalErrorneousReadCount << "\n"
- << "per read error rate " << 100.0 * totalErrorneousReadCount
/ totalReadCount << "\n"
- << "\n"
- << "total bases " << totalBaseCount << "\n"
---- seqan2.orig/apps/gustaf/msplazer_main.h
-+++ seqan2/apps/gustaf/msplazer_main.h
-@@ -194,7 +194,7 @@
- ++sizeCount[length(stellarMatches[i].matches)];
- }
- for(unsigned i = 0; i < length(sizeCount); ++ i){
-- std::cout << "Number of occurences for matches " << i << " : " <<
sizeCount[i] << std::endl;
-+ std::cout << "Number of occurrences for matches " << i << " : " <<
sizeCount[i] << std::endl;
- }
- for(unsigned i = 0; i < length(distanceScores); ++i){
- TScoreAlloc scores = distanceScores[i];
---- seqan2.orig/apps/seqcons2/seqcons_options.cpp
-+++ seqan2/apps/seqcons2/seqcons_options.cpp
-@@ -122,7 +122,7 @@
- << "OVERLAP WINDOW SIZE \t" << overlapWindowSize << "\n"
- << "\n"
- << "K-MER SIZE \t" << kMerSize << "\n"
-- << "K-MER MAX OCCURENCES \t" << kMerMaxOcc << "\n"
-+ << "K-MER MAX OCCURRENCES \t" << kMerMaxOcc << "\n"
- << "\n"
- << "REALIGNMENT BANDWIDTH \t" << reAlignmentBandwidth << "\n"
- << "REALIGNMENT ENVIRONMENT\t" << reAlignmentEnvironment << "\n";
-@@ -208,7 +208,7 @@
- setMinValue(parser, "k-mer-size", "5");
- setDefaultValue(parser, "k-mer-size", "20");
-
-- addOption(parser, seqan::ArgParseOption("", "k-mer-max-occ", "Ignore
k-mer with higher occurence count, 0 to disable.",
-+ addOption(parser, seqan::ArgParseOption("", "k-mer-max-occ", "Ignore
k-mer with higher occurrence count, 0 to disable.",
- seqan::ArgParseOption::INTEGER,
"COUNT"));
- setMinValue(parser, "k-mer-max-occ", "0");
- setDefaultValue(parser, "k-mer-max-occ", "200");
---- seqan2.orig/apps/seqcons2/seqcons_options.h
-+++ seqan2/apps/seqcons2/seqcons_options.h
-@@ -100,7 +100,7 @@
-
- // K-mer length to use for identifying overlap candidates.
- int kMerSize;
-- // K-mers with a higher number of occurences are ignored.
-+ // K-mers with a higher number of occurrences are ignored.
- int kMerMaxOcc;
-
- // -----------------------------------------------------------------------
---- seqan2.orig/apps/seqcons2/tests/alns1.contig_consensus.sam.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.contig_consensus.sam.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/alns1.contig_consensus.txt.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.contig_consensus.txt.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/alns1.nop.sam.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.nop.sam.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/alns1.nop.txt.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.nop.txt.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/alns1.overlap_consensus.sam.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.overlap_consensus.sam.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/alns1.overlap_consensus.txt.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.overlap_consensus.txt.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/alns1.pos_consensus.sam.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.pos_consensus.sam.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/alns1.pos_consensus.txt.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.pos_consensus.txt.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/alns1.realign.sam.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.realign.sam.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/alns1.realign.txt.stderr
-+++ seqan2/apps/seqcons2/tests/alns1.realign.txt.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/seqs1.align_consensus.stderr
-+++ seqan2/apps/seqcons2/tests/seqs1.align_consensus.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/seqs1.nop.stderr
-+++ seqan2/apps/seqcons2/tests/seqs1.nop.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
-+++ seqan2/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/seqs2.align_consensus.sam.stderr
-+++ seqan2/apps/seqcons2/tests/seqs2.align_consensus.sam.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/seqcons2/tests/seqs2.align_consensus.txt.stderr
-+++ seqan2/apps/seqcons2/tests/seqs2.align_consensus.txt.stderr
-@@ -16,7 +16,7 @@
- OVERLAP WINDOW SIZE 20
-
- K-MER SIZE 20
--K-MER MAX OCCURENCES 200
-+K-MER MAX OCCURRENCES 200
-
- REALIGNMENT BANDWIDTH 10
- REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/stellar/README
-+++ seqan2/apps/stellar/README
-@@ -182,7 +182,7 @@
- Remove overabundant query k-mers from the k-mer index. NUM must be a
- value between 0 (remove all) and 1 (remove nothing, default). k-mers with
- a relative abundance above NUM are removed. The relative abundance is
-- the absolute number of a k-mers occurences divided by the total number of
-+ the absolute number of a k-mers occurrences divided by the total number of
- k-mers in the query sequence(s). The total number of k-mers is about
- the total length of the query sequence(s).
-
---- seqan2.orig/demos/tutorial/basics/strings.cpp
-+++ seqan2/demos/tutorial/basics/strings.cpp
-@@ -22,7 +22,7 @@
- }
- std::cout << std::endl;
- //![iterate-and-replace]
--//![count-occurences]
-+//![count-occurrences]
- typedef Size<TAminoAcidString>::Type TSize;
- typedef String<TSize> TCounterString;
- TCounterString counter;
-@@ -30,7 +30,7 @@
- resize(counter, alphSize, 0);
- for (TIter it = begin(sourceSeq); it != itEnd; goNext(it))
- value(counter, ordValue(value(it))) += 1;
--//![count-occurences]
-+//![count-occurrences]
- //![frequency-table]
- typedef Iterator<TCounterString>::Type TCounterIter;
- TCounterIter countIt = begin(counter);
---- seqan2.orig/dox/pages/suffix_array.dox
-+++ seqan2/dox/pages/suffix_array.dox
-@@ -13,7 +13,7 @@
- * "Faster Suffix Sorting", 1999), and a quicksort based algorithm.
- *
- * The following example constructs a suffix array using the modified Skew
algorithm and searches the interval of suffices
-- * beginning with $t="l"$. The start positions of these suffices are the
occurences of $t$, which are outputted at last.
-+ * beginning with $t="l"$. The start positions of these suffices are the
occurrences of $t$, which are outputted at last.
- * This is only an example for @link createSuffixArray @endlink and similar
functions. For an index based substring search
- * better use the more generic @link Finder @endlink class (see @Demo.Index
Finder@ demo).
- *
---- seqan2.orig/include/seqan/find/find_base.h
-+++ seqan2/include/seqan/find/find_base.h
-@@ -187,9 +187,9 @@
- * @param[in] k Desired minimal score (for approximate matching).
<tt>k</tt> is a number <tt><= 0</tt>.
- * Differences are deletions, insertions, and
substitutions.
- *
-- * @return bool <tt>true</tt> if an occurence was found and <tt>false</tt> if
not.
-+ * @return bool <tt>true</tt> if an occurrence was found and <tt>false</tt>
if not.
- *
-- * Repeated calls of this function iterate through all occurences of
<tt>pattern</tt>.
-+ * Repeated calls of this function iterate through all occurrences of
<tt>pattern</tt>.
- *
- * @section Examples
- *
---- seqan2.orig/include/seqan/find/find_begin.h
-+++ seqan2/include/seqan/find/find_begin.h
-@@ -344,7 +344,7 @@
- * @param[in,out] finder The Finder object to search through.
- * @param[in,out] pattern The Pattern object to search for. This must be a
pattern for approximate string matching.
- * @param[in] limit The score limit. The default is the limit used
during the last <tt>find</tt> call, see
-- * <tt>getScore</tt>. All occurences that score at
least <tt>limit</tt> are reported.
-+ * <tt>getScore</tt>. All occurrences that score at
least <tt>limit</tt> are reported.
- *
- * @return bool <tt>true</tt> indicates a match, <tt>false</tt> indicates no
match.
- *
---- seqan2.orig/include/seqan/index/index_esa_algs_multi.h
-+++ seqan2/include/seqan/index/index_esa_algs_multi.h
-@@ -486,7 +486,7 @@
-
-
- template <typename TSTree>
-- class Iter< MultiMem<TSTree>, MultiMemOccurences > {
-+ class Iter< MultiMem<TSTree>, MultiMemOccurrences > {
- public:
-
- typedef typename Value<TSTree>::Type TValue;
-@@ -687,21 +687,21 @@
-
-
- template < typename TRepeat >
-- inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type &
-- value(Iter<TRepeat, MultiMemOccurences> const &it) {
-+ inline typename Value< Iter<TRepeat, MultiMemOccurrences> >::Type &
-+ value(Iter<TRepeat, MultiMemOccurrences> const &it) {
- return it.tmp;
- }
-
- template < typename TRepeat >
-- inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type &
-- value(Iter<TRepeat, MultiMemOccurences> &it) {
-+ inline typename Value< Iter<TRepeat, MultiMemOccurrences> >::Type &
-+ value(Iter<TRepeat, MultiMemOccurrences> &it) {
- return it.tmp;
- }
-
- //TODO:fix me
- template < typename TRepeat >
-- inline Iter<TRepeat, MultiMemOccurences> &
-- goNext(Iter<TRepeat, MultiMemOccurences> &it) {
-+ inline Iter<TRepeat, MultiMemOccurrences> &
-+ goNext(Iter<TRepeat, MultiMemOccurrences> &it) {
- if (it._innerStep()) {
- // it.tmp.i1 = saAt(it.subState.parentPtr, container(*it.mmemIt));
- // it.tmp.i2 = saAt(it.subState.childPtr, container(*it.mmemIt));
-@@ -715,23 +715,23 @@
- }
-
- template < typename TRepeat >
-- inline bool atEnd(Iter<TRepeat, MultiMemOccurences> const &it) {
-+ inline bool atEnd(Iter<TRepeat, MultiMemOccurrences> const &it) {
- return it._atEnd;
- }
-
- template < typename TRepeat >
-- inline bool atEnd(Iter<TRepeat, MultiMemOccurences> &it) {
-+ inline bool atEnd(Iter<TRepeat, MultiMemOccurrences> &it) {
- return it._atEnd;
- }
-
-
- template <typename TSTree>
- struct Iterator< MultiMem<TSTree> > {
-- typedef Iter<MultiMem<TSTree>, MultiMemOccurences> Type;
-+ typedef Iter<MultiMem<TSTree>, MultiMemOccurrences> Type;
- };
-
- template <typename TSTree>
-- struct Size< Iter<MultiMem<TSTree>, MultiMemOccurences> > {
-+ struct Size< Iter<MultiMem<TSTree>, MultiMemOccurrences> > {
- typedef typename Size<TSTree>::Type Type;
- };
-
---- seqan2.orig/include/seqan/index/index_fm_dox.h
-+++ seqan2/include/seqan/index/index_fm_dox.h
-@@ -475,7 +475,7 @@
- * @param[in] character The character.
- * @param[in] pos The position (which is included in the counting).
- *
-- * @return TSize The number of occurences (Metafunction: @link Index#Size
@endlink).
-+ * @return TSize The number of occurrences (Metafunction: @link Index#Size
@endlink).
- */
-
- /*!
---- seqan2.orig/include/seqan/statistics/statistics_base.h
-+++ seqan2/include/seqan/statistics/statistics_base.h
-@@ -83,13 +83,13 @@
- }
-
- /*
-- * @fn _numOccurences
-+ * @fn _numOccurrences
- * @headerfile <seqan/statistics.h>
-- * @brief Auxiliary function to compute the number of occurences of a set of
patterns in a set of text strings.
-+ * @brief Auxiliary function to compute the number of occurrences of a set of
patterns in a set of text strings.
- *
-- * @signature void _numOccurences(W, haystack, needle, algoTag);
-+ * @signature void _numOccurrences(W, haystack, needle, algoTag);
- *
-- * @param[in,out] W A counter, incremented by the number of occurences.
-+ * @param[in,out] W A counter, incremented by the number of
occurrences.
- * @param[in] haystack The text strings.
- * @param[in] needle The set of patterns.
- * @param[in] algoTag The tag to select the online text search algorithm
with.
---- seqan2.orig/apps/sgip/sgip.cpp
-+++ seqan2/apps/sgip/sgip.cpp
-@@ -72,7 +72,7 @@
- struct SgipOption
- {
- // I/O options.
-- CharString orginalFile; // name of orginal file(first graph)
-+ CharString originalFile; // name of original file(first graph)
- CharString comparFile; // name of comparisive file(second graph)
- CharString outputFile; // name of result file
- CharString compareFolder;
-@@ -82,8 +82,8 @@
- FileOption activeFile;
- SearchingType searchingType;
- CharString algorithm; // Search strategy for metric
dimension,e.g. Greedy, genetic etc.
-- unsigned odimension; // metric dimension of orginal graph
specified by user
-- unsigned cdimension; // metric dimension of comparitive graph
specified by user
-+ unsigned odimension; // metric dimension of original graph
specified by user
-+ unsigned cdimension; // metric dimension of comparative graph
specified by user
- bool showHelp;
- bool showVersion;
- bool isoCheck; //to check whether two input graphs are
isomorphic
-@@ -127,7 +127,7 @@
- char const * file1, * file2;
- if (!options.isoCheck)
- {
-- file1 = toCString(options.orginalFile);
-+ file1 = toCString(options.originalFile);
- if (!_createGraph(g1, SivaLab(), file1))
- return 1;
-
-@@ -137,7 +137,7 @@
- }
- else
- {
-- file1 = toCString(options.orginalFile);
-+ file1 = toCString(options.originalFile);
- file2 = toCString(options.comparFile);
- if (!_createGraph(g1, SivaLab(), file1))
- return 1;
-@@ -169,9 +169,9 @@
- {
- setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
- addDescription(parser, " SGIP - Solution of Graph Isomorphism Problem");
-- addUsageLine(parser, "-o <orginal graph> [Option]");
-+ addUsageLine(parser, "-o <original graph> [Option]");
- addSection(parser, "Mandatory Options");
-- addOption(parser, ArgParseOption("o", "orginal", "File containing orginal
graph", ArgParseArgument::INPUT_FILE,"IN"));
-+ addOption(parser, ArgParseOption("o", "original", "File containing
original graph", ArgParseArgument::INPUT_FILE,"IN"));
- setRequired(parser, "o");
- addSection(parser, "Main Options");
- addOption(parser, ArgParseOption("a", "algorithm", "Algorithm used for
searching metric dimension", ArgParseArgument::STRING));
-@@ -179,10 +179,10 @@
- addOption(parser, ArgParseOption("s", "searching", "Searching algorithm
used for detecting resolving set,heuristic 0 bruteforce 1.",
ArgParseArgument::INTEGER));
- setDefaultValue(parser, "searching", "0");
- addOption(parser, ArgParseOption("i", "isomorphism", "To check whether
two given graphs are isomorphic"));
-- addOption(parser, ArgParseOption("c", "comparitive", "File containing
comparitive graph", ArgParseArgument::INPUT_FILE,"IN"));
-- addOption(parser, ArgParseOption("od", "odimension", "Specified initial
dimension of orginal graph by user", ArgParseArgument::INTEGER));
-+ addOption(parser, ArgParseOption("c", "comparative", "File containing
comparative graph", ArgParseArgument::INPUT_FILE,"IN"));
-+ addOption(parser, ArgParseOption("od", "odimension", "Specified initial
dimension of original graph by user", ArgParseArgument::INTEGER));
- setDefaultValue(parser, "odimension", "3");
-- addOption(parser, ArgParseOption("cd", "cdimension", "Specified initial
dimension of comparitive graph by user", ArgParseArgument::INTEGER));
-+ addOption(parser, ArgParseOption("cd", "cdimension", "Specified initial
dimension of comparative graph by user", ArgParseArgument::INTEGER));
- setDefaultValue(parser, "cdimension", "3");
- addOption(parser, ArgParseOption("ad", "directory", "test for all graphs
in a specified directory", ArgParseArgument::STRING));
- addOption(parser, ArgParseOption("v", "verbose", "control the level of
output files ", ArgParseArgument::INTEGER));
-@@ -212,14 +212,14 @@
- return res;
-
- // Extract option value.
-- getOptionValue(options.orginalFile, parser, "o");
-+ getOptionValue(options.originalFile, parser, "o");
- if (isSet(parser, "i"))
- {
- if (!isSet(parser, "c"))
- {
- if (!isSet(parser, "ad"))
- {
-- std::cerr << "sgip" << ":comparitive file has not been
specified!" << std::endl;
-+ std::cerr << "sgip" << ":comparative file has not been
specified!" << std::endl;
- printShortHelp(parser, std::cerr);
- return ArgumentParser::PARSE_ERROR;
- }
---- seqan2.orig/apps/gustaf/msplazer_out.h
-+++ seqan2/apps/gustaf/msplazer_out.h
-@@ -1125,7 +1125,7 @@
- std::cout << "Thresholds:" << std::endl;
- std::cout << " overlap threshold (oth) : " << options.simThresh
<< std::endl;
- std::cout << " gap threshold (gth) : " << options.gapThresh
<< std::endl;
-- std::cout << " inital gap threshold (ith) : " <<
options.initGapThresh << std::endl;
-+ std::cout << " initial gap threshold (ith) : " <<
options.initGapThresh << std::endl;
- std::cout << "Penalties:" << std::endl;
- std::cout << " translocation penalty (tp) : " << options.diffDBPen
<< std::endl;
- std::cout << " inversion penalty (ip) : " <<
options.diffStrandPen << std::endl;
---- seqan2.orig/apps/gustaf/tests/pairedEnd_st1_l30.stdout
-+++ seqan2/apps/gustaf/tests/pairedEnd_st1_l30.stdout
-@@ -6,7 +6,7 @@
- Thresholds:
- overlap threshold (oth) : 0.5
- gap threshold (gth) : 5
-- inital gap threshold (ith) : 15
-+ initial gap threshold (ith) : 15
- Penalties:
- translocation penalty (tp) : 5
- inversion penalty (ip) : 5
---- seqan2.orig/apps/gustaf/tests/reference2_st1_l30.stdout
-+++ seqan2/apps/gustaf/tests/reference2_st1_l30.stdout
-@@ -5,7 +5,7 @@
- Thresholds:
- overlap threshold (oth) : 0.5
- gap threshold (gth) : 5
-- inital gap threshold (ith) : 15
-+ initial gap threshold (ith) : 15
- Penalties:
- translocation penalty (tp) : 5
- inversion penalty (ip) : 5
---- seqan2.orig/apps/gustaf/tests/st1_l30.stdout
-+++ seqan2/apps/gustaf/tests/st1_l30.stdout
-@@ -5,7 +5,7 @@
- Thresholds:
- overlap threshold (oth) : 0.5
- gap threshold (gth) : 5
-- inital gap threshold (ith) : 15
-+ initial gap threshold (ith) : 15
- Penalties:
- translocation penalty (tp) : 5
- inversion penalty (ip) : 5
---- seqan2.orig/apps/gustaf/tests/st1_l30_gth3.stdout
-+++ seqan2/apps/gustaf/tests/st1_l30_gth3.stdout
-@@ -5,7 +5,7 @@
- Thresholds:
- overlap threshold (oth) : 0.5
- gap threshold (gth) : 3
-- inital gap threshold (ith) : 15
-+ initial gap threshold (ith) : 15
- Penalties:
- translocation penalty (tp) : 5
- inversion penalty (ip) : 5
---- seqan2.orig/apps/gustaf/tests/st1_l30_ith5.stdout
-+++ seqan2/apps/gustaf/tests/st1_l30_ith5.stdout
-@@ -5,7 +5,7 @@
- Thresholds:
- overlap threshold (oth) : 0.5
- gap threshold (gth) : 5
-- inital gap threshold (ith) : 5
-+ initial gap threshold (ith) : 5
- Penalties:
- translocation penalty (tp) : 5
- inversion penalty (ip) : 5
---- seqan2.orig/apps/gustaf/tests/st1_l30_m.stdout
-+++ seqan2/apps/gustaf/tests/st1_l30_m.stdout
-@@ -5,7 +5,7 @@
- Thresholds:
- overlap threshold (oth) : 0.5
- gap threshold (gth) : 5
-- inital gap threshold (ith) : 15
-+ initial gap threshold (ith) : 15
- Penalties:
- translocation penalty (tp) : 5
- inversion penalty (ip) : 5
---- seqan2.orig/apps/gustaf/tests/st2_l100.stdout
-+++ seqan2/apps/gustaf/tests/st2_l100.stdout
-@@ -5,7 +5,7 @@
- Thresholds:
- overlap threshold (oth) : 0.5
- gap threshold (gth) : 5
-- inital gap threshold (ith) : 15
-+ initial gap threshold (ith) : 15
- Penalties:
- translocation penalty (tp) : 5
- inversion penalty (ip) : 5
----
seqan2.orig/manual/source/Tutorial/Algorithms/Alignment/PairwiseSequenceAlignment.rst
-+++
seqan2/manual/source/Tutorial/Algorithms/Alignment/PairwiseSequenceAlignment.rst
-@@ -496,7 +496,7 @@
- Complete Solution (and more explanations)
- .. container:: foldable
-
-- Write the `main` body of the program with type definition and
initalization of the used data structures.
-+ Write the `main` body of the program with type definition and
initialization of the used data structures.
-
- .. includefrags::
demos/tutorial/pairwise_sequence_alignment/assignment5.cpp
- :fragment: main
---- seqan2.orig/apps/mason2/mason_options.cpp
-+++ seqan2/apps/mason2/mason_options.cpp
-@@ -883,22 +883,22 @@
- setDefaultValue(parser, "sanger-quality-match-end-stddev", "2");
-
- addOption(parser, seqan::ArgParseOption("",
"sanger-quality-error-start-mean",
-- "Mean PHRED quality for
errorneous bases of first base in Sanger sequencing.",
-+ "Mean PHRED quality for erroneous
bases of first base in Sanger sequencing.",
- seqan::ArgParseOption::DOUBLE,
"QUAL"));
- setDefaultValue(parser, "sanger-quality-error-start-mean", "30");
-
- addOption(parser, seqan::ArgParseOption("",
"sanger-quality-error-end-mean",
-- "Mean PHRED quality for
errorneous bases of last base in Sanger sequencing.",
-+ "Mean PHRED quality for erroneous
bases of last base in Sanger sequencing.",
- seqan::ArgParseOption::DOUBLE,
"QUAL"));
- setDefaultValue(parser, "sanger-quality-error-end-mean", "20");
-
- addOption(parser, seqan::ArgParseOption("",
"sanger-quality-error-start-stddev",
-- "Mean PHRED quality for
errorneous bases of first base in Sanger sequencing.",
-+ "Mean PHRED quality for erroneous
bases of first base in Sanger sequencing.",
- seqan::ArgParseOption::DOUBLE,
"QUAL"));
- setDefaultValue(parser, "sanger-quality-error-start-stddev", "2");
-
- addOption(parser, seqan::ArgParseOption("",
"sanger-quality-error-end-stddev",
-- "Mean PHRED quality for
errorneous bases of last base in Sanger sequencing.",
-+ "Mean PHRED quality for erroneous
bases of last base in Sanger sequencing.",
- seqan::ArgParseOption::DOUBLE,
"QUAL"));
- setDefaultValue(parser, "sanger-quality-error-end-stddev", "5");
- }
---- seqan2.orig/apps/razers/razers.h
-+++ seqan2/apps/razers/razers.h
-@@ -225,7 +225,7 @@
-
- if (TSpec::DUMP_VERIFICATION_TASKS)
- {
-- open(verifications, "verfication_tasks.bin",
OPEN_WRONLY|OPEN_CREATE);
-+ open(verifications, "verification_tasks.bin",
OPEN_WRONLY|OPEN_CREATE);
- }
- }
- };
---- seqan2.orig/apps/razers/razers_matepairs.h
-+++ seqan2/apps/razers/razers_matepairs.h
-@@ -795,7 +795,7 @@
- ::std::cerr << ::std::endl;
- ::std::cerr << "___FILTRATION_STATS____" << ::std::endl;
- ::std::cerr << "Filtration counter: " << options.FP +
options.TP << ::std::endl;
-- ::std::cerr << "Successful verfications: " << options.TP <<
::std::endl;
-+ ::std::cerr << "Successful verifications: " << options.TP <<
::std::endl;
- }
- return 0;
- }
---- seqan2.orig/apps/razers3/razers.h
-+++ seqan2/apps/razers3/razers.h
-@@ -3101,7 +3101,7 @@
- std::cerr << std::endl;
- std::cerr << "___FILTRATION_STATS____" << std::endl;
- std::cerr << "Filtration counter: " << options.countFiltration
<< std::endl;
-- std::cerr << "Successful verfications: " << options.countVerification
<< std::endl;
-+ std::cerr << "Successful verifications: " <<
options.countVerification << std::endl;
- }
- return 0;
- }
---- seqan2.orig/apps/razers3/razers_matepairs.h
-+++ seqan2/apps/razers3/razers_matepairs.h
-@@ -1156,7 +1156,7 @@
- std::cerr << std::endl;
- std::cerr << "___FILTRATION_STATS____" << std::endl;
- std::cerr << "Filtration counter: " << options.countFiltration <<
std::endl;
-- std::cerr << "Verfication counter: " << options.countVerification <<
std::endl;
-+ std::cerr << "Verification counter: " << options.countVerification <<
std::endl;
- }
-
- return 0;
---- seqan2.orig/apps/razers3/razers_matepairs_parallel.h
-+++ seqan2/apps/razers3/razers_matepairs_parallel.h
-@@ -1623,7 +1623,7 @@
- std::cerr << std::endl;
- std::cerr << "___FILTRATION_STATS____" << std::endl;
- std::cerr << "Filtration counter: " << options.countFiltration <<
std::endl;
-- std::cerr << "Verfication counter: " << options.countVerification <<
std::endl;
-+ std::cerr << "Verification counter: " << options.countVerification <<
std::endl;
- }
-
- // Restore global state.
---- seqan2.orig/apps/razers3/razers_parallel.h
-+++ seqan2/apps/razers3/razers_parallel.h
-@@ -1163,7 +1163,7 @@
- std::cerr << std::endl;
- std::cerr << "___FILTRATION_STATS____" << std::endl;
- std::cerr << "Filtration counter: " << options.countFiltration
<< std::endl;
-- std::cerr << "Successful verfications: " << options.countVerification
<< std::endl;
-+ std::cerr << "Successful verifications: " <<
options.countVerification << std::endl;
- }
-
- // Restore global state.
---- seqan2.orig/apps/rep_sep/rep_sep.cpp
-+++ seqan2/apps/rep_sep/rep_sep.cpp
-@@ -73,7 +73,7 @@
- addUsageLine(parser, "[OPTION]... --assembly <input file> --output-prefix
<prefix>");
- setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
- setDate(parser, SEQAN_DATE);
-- setShortDescription(parser, "Repeat Seperation Tool -- Copyright (c)
2009, Stephan Aiche");
-+ setShortDescription(parser, "Repeat Separation Tool -- Copyright (c)
2009, Stephan Aiche");
-
- // needed input file
- addOption(parser, ArgParseOption("a", "assembly", "Input assembly
filename.", ArgParseArgument::INPUT_FILE));
---- seqan2.orig/include/seqan/blast/blast_tabular_in.h
-+++ seqan2/include/seqan/blast/blast_tabular_in.h
-@@ -74,7 +74,7 @@
- Possibly other lines can be written as comments.
-
- Because 0 matches are allowed, multiple COMMENTLINES can succeed each other,
the
--criterium for seperation employed by this implementation is that an NCBI Blast
-+criterium for separation employed by this implementation is that an NCBI Blast
- COMMENTLINES always ends after the "Fields" line and NCBI Blast+ COMMENTLINES
end after
- the "number of hits"-line.
- */
---- seqan2.orig/apps/stellar/stellar.cpp
-+++ seqan2/apps/stellar/stellar.cpp
-@@ -262,7 +262,7 @@
-
- std::cout << "Loaded " << seqCount << " " << name << " sequence" <<
((seqCount > 1) ? "s." : ".") << std::endl;
- if (!idsUnique)
-- std::cerr << "WARNING: Non-unique " << name << " ids. Output can be
ambigous.\n";
-+ std::cerr << "WARNING: Non-unique " << name << " ids. Output can be
ambiguous.\n";
- return true;
- }
-
diff --git a/debian/patches/tandem-rename b/debian/patches/tandem-rename
deleted file mode 100644
index 50e626c..0000000
--- a/debian/patches/tandem-rename
+++ /dev/null
@@ -1,54 +0,0 @@
-From: Michael R. Crusoe <michael.cru...@gmail.com>
-Subject: Work around GNU Hurd's TANDEM constant
-https://fossies.org/dox/glibc-2.24/sysdeps_2mach_2hurd_2bits_2ioctls_8h.html#aea2b0b2a11b94d258198cd2104bc79a4
---- seqan2.orig/apps/gustaf/msplazer.h
-+++ seqan2/apps/gustaf/msplazer.h
-@@ -134,7 +134,7 @@
- INSERTION, // 1
- DELETION, // 2
- INVERSION, // 3
-- TANDEM, // 4
-+ SEQAN_TANDEM, // 4 TANDEM is an IOCTL numeric constant in Hurd
- DISPDUPLICATION, // 5
- INTERTRANSLOCATION, // 6
- TRANSLOCATION, // 7
-@@ -696,7 +696,7 @@
- case TBreakpoint::INVERSION:
- out << "SVType: inversion";
- break;
-- case TBreakpoint::TANDEM:
-+ case TBreakpoint::SEQAN_TANDEM:
- out << "SVType: tandem";
- break;
- case TBreakpoint::DISPDUPLICATION:
---- seqan2.orig/apps/gustaf/msplazer_algorithms.h
-+++ seqan2/apps/gustaf/msplazer_algorithms.h
-@@ -493,7 +493,7 @@
- // Double overlap check (not handled jet)
- // std::cerr << "double overlap in reference and read
called from read overlap" << std::endl;
- // std::cout << "Translocation double overlap" <<
std::endl;
-- bp.svtype = TBreakpoint::TANDEM;
-+ bp.svtype = TBreakpoint::SEQAN_TANDEM;
- }
-
- //std::cout << "Breakpoint " << bp << std::endl;
---- seqan2.orig/apps/gustaf/msplazer_out.h
-+++ seqan2/apps/gustaf/msplazer_out.h
-@@ -196,7 +196,7 @@
- case TBreakpoint::INVERSION:
- record.type = "inversion";
- break;
-- case TBreakpoint::TANDEM:
-+ case TBreakpoint::SEQAN_TANDEM:
- record.type = "tandem";
- break;
- case TBreakpoint::DISPDUPLICATION:
-@@ -647,7 +647,7 @@
- case TBreakpoint::INVERSION:
- _fillVcfRecordInversion(record, bp, ref, id);
- return 1;
-- case TBreakpoint::TANDEM:
-+ case TBreakpoint::SEQAN_TANDEM:
- _fillVcfRecordTandem(record, bp, ref, id);
- return 1;
- case TBreakpoint::DISPDUPLICATION:
diff --git a/debian/patches/typo-fix b/debian/patches/typo-fix
deleted file mode 100644
index 2d8ff2d..0000000
--- a/debian/patches/typo-fix
+++ /dev/null
@@ -1,22 +0,0 @@
-From: Michael R. Crusoe <michael.cru...@gail.com
-Subject: Fix typo
---- seqan2.orig/include/seqan/parallel/parallel_lock.h
-+++ seqan2/include/seqan/parallel/parallel_lock.h
-@@ -218,14 +218,14 @@
- #elif defined(__arm__) || defined(__aarch64__) // ARM.
- __asm__ __volatile__ ("yield" ::: "memory");
- #elif defined(__sparc) || defined(__sparc__) // SPARC
--#if definde(__SUNPRO_C)
-+#if defined(__SUNPRO_C)
- __asm __volatile__ ("rd %%ccr, %%g0\n\t"
- "rd %%ccr, %%g0\n\t"
-- "rd %%ccr, %%g0")
-+ "rd %%ccr, %%g0");
- #else
- __asm __volatile__ ("rd %ccr, %g0\n\t"
- "rd %ccr, %g0\n\t"
-- "rd %ccr, %g0")
-+ "rd %ccr, %g0");
- #endif // defined(__SUNPRO_C)
- #elif defined(__ppc__) || defined(__ppc64__) || defined(_ARCH_PPC) ||
defined(_ARCH_PPC64) // PowerPC
- __asm__ __volatile__ ("or 27,27,27" ::: "memory");
--
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